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The error rates that I found on the calibration files are given in percentage, but I couldn't find whether it is calculated on full-scale (% FS) or on percentage of reading (% RD). If I do $20000$ shots and found $|00\rangle$ at $5000$ with an error rate of $1\%$, should it be $5000 \pm 200$ or $5000 \pm 50$? Thank you!

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The percentage error rates in the calibration files give the average readout error across all qubits. So, in your example, $20000$ shots of which $5000$ measured $|00\rangle$ on a backend with an average qubit error rate of $1\%$ would correspond to an estimated uncertainty of $5000 \pm 50$. To more accurately quantify measurement uncertainty you'll want to look at the single-qubit error rate for each qubit and the CNOT error rate for each connection, see How to get the CNOT error rate between 2 qubits on a given IBMQ Backend? and Is current information about readout-errors of qubits on IBM quantum devices available on some internet page?

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